The Doctor and Her Companion
by Dreamin
Summary: The Doctor decides to make war criminal Khan her next companion. Khanolly. Doctor Who AU.


A/N: This was inspired by a prompt from welcometonightcourt: "doctor and companion au." I decided Molly would be great as the Fourteenth Doctor.

* * *

If there was one thing the Doctor hated, it was seeing a life, any life, wasted. That was her main reason for stepping in when the war criminal Khan Noonien Singh was sentenced to spend the rest of his existence in cryogenic suspension.

That and the fact that he was the handsomest man she'd ever seen.

Firmly setting her hormones aside, she convinced the Admiralty to let her take him and his frozen crew, promising to never let them near Federation Space again.

As soon as his crew's pods were safely stored on board the TARDIS, Khan locked himself in his quarters. The Doctor had anticipated that – she had taken the time to install a replicator in his kitchen before she took him on so he would be able to eat without having to face her.

Consequentially, it was almost a week before she saw him again. She had just gotten out of the pool and was walking down the hallway when she quite literally ran into Khan. Compared to her slight, petite frame, he was a mountain of solid muscle. The impact would have knocked her on her bum if his strong arms hadn't shot out and grabbed her shoulders, steadying her.

His nearness combined with her embarrassment caused her to blush furiously. "Um, sorry, I should watch where I'm going." _I'm thousands of years old, I shouldn't be acting like a silly teenager._

"I'm just as guilty." He assessed her for a moment, taking in her yellow bikini top and the purple towel wrapped around her waist. Khan raised an eyebrow, smiling a bit. "You don't look like any sort of Oncoming Storm."

She huffed in annoyance. "You're not threatening anyone under my protection. Ask any Dalek, they'll tell you how scary I am." She waved a hand to indicate her current form. "Just because this body makes me look like I'm all glitter and rainbows, that doesn't mean I can't be ruthless when I need to be."

Khan chuckled. "I'm not complaining. Good day, Doctor." He started walking away.

The Doctor rolled her eyes. _Men. Even when I was one, I didn't understand them._

* * *

A week later, she decided to check on his crew. The pods were programmed to give a warning alarm if anything went wrong, but the Doctor still wanted to see for herself. As soon as she walked into the cavernous cargo bay where they were kept, she saw Khan looking over one of the pods. She would've turned around and left him alone with them, but the look on his face stopped her. She had never in all her years seen anyone that lost and alone. She approached him slowly, stopping about a foot away when he finally looked up at her, his expression unchanged.

"We can wake them up, if you want," she said gently. "The TARDIS Is big enough for everyone."

"To what end?" he asked quietly. "We didn't want to endlessly tour the stars, we wanted a place we could settle."

"Then I can find you an uninhabited planet."

He looked at her for a moment then simply nodded.

* * *

Finding an uninhabited and unclaimed planet far from Federation Space wasn't easy, but she did it. The two of them carefully worked to wake his crew then she let Khan explain the situation to them. The TARDIS landed on their new home and the Doctor insisted on helping them set up their colony with materials and supplies she provided.

Every night, Khan had dinner with her while they talked about the progress they were making. One night, six months after they had first landed on the planet, he was quieter than usual.

"Penny for your thoughts?" she asked, smiling a bit.

"The colony will be on its feet soon."

"Yes, you should be proud." The Doctor tilted her head a bit. "You're not happy, why?"

"It doesn't matter," he said firmly.

When she tried to press the issue, he got annoyed and left the TARDIS.

* * *

When the colony was ready to be self-sustaining, the colonists threw a banquet in the Doctor's honor to thank her. They held it at night, on tables under the stars. She sat beside Khan during the meal, trying hard not to stare at him all night. Even though she had already committed his face and form to memory, she still wanted more.

After the meal, the musicians amongst the colonists started playing and others started to dance. The Doctor glanced at Khan but she knew that the leader of the colonists would never do something as "undignified" as dancing.

One of the male colonists, Tayton, came over to them, smiling, and held out his hand to her. "May I have this dance, Doctor?"

She was about to say yes when Khan took her hand. "I'm afraid the lady is spoken for, Tayton."

The other man just smirked then went over to one of the female colonists and asked her to dance.

The Doctor looked at Khan, one eyebrow raised. "I didn't realize I was spoken for. When did that happen?"

"Just now," he muttered.

"Ah," she said, grinning, "and who did the speaking?"

Khan huffed in annoyance then rose and offered her his hand. She took it and stood up, her grin never wavering as he led her to where the others were dancing. It was a slow song and the Doctor loved the feeling of being in his arms.

"Will you let me lead?" he muttered after a moment.

She blushed, smiling a bit. "Sorry, this is only my second female body, I'm used to leading." She let him take the lead.

He murmured, "Do you really have no other name than 'Doctor?'"

"When I'm undercover and need a name, I go by Molly Hooper."

He gazed at her. "May I call you that, then?"

She smiled softly. "Yes, that's fine."

Khan lowered his head and was about to kiss her when a firework went off, making both of them jump. The Doctor giggled as Khan glowered at the offending fireworks display overhead, then he looked at her and joined in her laughter.

At the end of the banquet, he walked her back to the TARDIS.

"I'd invite you in," she said softly, "but it's probably not a good idea."

He nodded. "My place is here, your place is among the stars."

"I'll come back to visit. I'll be here so often you'll get sick of me."

"Never," Khan murmured, then he took her in his arms and kissed her deeply.

The Doctor kissed him back, wanting to hold on to this one perfect moment. But like all such moments, it had to end. After one final kiss, she told him she'd see him soon then she boarded the TARDIS and left the man she loved behind.

* * *

To her, it was only a week before the message came, but she knew it was six months for the colonists. The message was simple – "Come back."

Never one to ignore a message, she landed the TARDIS on the planet and realized when she opened the door that it was the middle of winter. The colony seemed to be thriving, though – there were several more buildings than when she had left.

Bundling up in a coat, hat, gloves, and a scarf, she made her way through the snow to Khan's home. It was larger than the others and set apart from them. The Doctor took a deep breath before knocking on the door.

It opened after a moment then Khan was standing before her, staring at her for half a heartbeat before pulling her into his arms and snogging her breathless.

When they both came up for air, she smiled at him happily. "I take it you weren't the one who summoned me."

Khan chuckled. "No, but I want to thank whoever it was who did. Molly, I've had a change of heart. Ever since you left, I've been miserable. I realized my place is with you, wherever that is."

She stared at him. "Khan, are you sure?"

"I'm positive. The others will be fine without me, but I won't be fine without you. That is, if you'll have me."

The Doctor beamed at him. "Of course I'll have you!"

She then proceeded to take him to the bedroom and had him multiple times that day.


End file.
